Uses of Class
com.compomics.util.parameters.identification.search.DigestionParameters

Packages that use DigestionParameters

Package	Description
com.compomics.util.experiment.biology.proteins	Classes related to proteins.
com.compomics.util.experiment.identification.features	Classes for the generation of identification features.
com.compomics.util.experiment.identification.filtering	Classes for the filtering of identification objects.
com.compomics.util.experiment.identification.protein_sequences.digestion	This package contains classes used to digest protein sequences into peptides.
com.compomics.util.parameters.identification.search	Identification parameters relative to the search.
com.compomics.util.parameters.identification.tool_specific	Parameters settings for the search algorithms.

Uses of DigestionParameters in com.compomics.util.experiment.biology.proteins

Methods in com.compomics.util.experiment.biology.proteins with parameters of type DigestionParameters

Modifier and Type	Method	Description
int	Peptide.getNMissedCleavages(DigestionParameters digestionPreferences)	Returns the number of missed cleavages using the digestion preferences.

Uses of DigestionParameters in com.compomics.util.experiment.identification.features

Methods in com.compomics.util.experiment.identification.features with parameters of type DigestionParameters

Modifier and Type	Method	Description
long[]	IdentificationFeaturesGenerator.getNonEnzymatic(long proteinMatchKey, DigestionParameters digestionPreferences)	Returns a list of non-enzymatic peptides for a given protein match.

Uses of DigestionParameters in com.compomics.util.experiment.identification.filtering

Methods in com.compomics.util.experiment.identification.filtering with parameters of type DigestionParameters

Modifier and Type	Method	Description
boolean	PeptideAssumptionFilter.validatePeptide(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, DigestionParameters digestionPreferences)	Validates the peptide based on the peptide length, the share of X's in the sequence and the allowed number of missed cleavages.

Uses of DigestionParameters in com.compomics.util.experiment.identification.protein_sequences.digestion

Methods in com.compomics.util.experiment.identification.protein_sequences.digestion with parameters of type DigestionParameters

Modifier and Type	Method	Description
SequenceIterator	IteratorFactory.getSequenceIterator(String sequence, DigestionParameters digestionPreferences, double massMin, double massMax)	Returns a sequence iterator for the given protein sequence and digestion preferences.

Uses of DigestionParameters in com.compomics.util.parameters.identification.search

Methods in com.compomics.util.parameters.identification.search that return DigestionParameters

Modifier and Type	Method	Description
static DigestionParameters	DigestionParameters.clone(DigestionParameters digestionParameters)	Clones the given parameters.
static DigestionParameters	DigestionParameters.getDefaultParameters()	Returns default digestion parameters.
DigestionParameters	SearchParameters.getDigestionParameters()	Returns the digestion preferences.

Methods in com.compomics.util.parameters.identification.search with parameters of type DigestionParameters

Modifier and Type	Method	Description
static DigestionParameters	DigestionParameters.clone(DigestionParameters digestionParameters)	Clones the given parameters.
boolean	DigestionParameters.isSameAs(DigestionParameters otherDigestionParameters)	Returns a boolean indicating whether these digestion parameters are the same as the given other parameters.
void	SearchParameters.setDigestionParameters(DigestionParameters digestionParameters)	Sets the digestion preferences.

Uses of DigestionParameters in com.compomics.util.parameters.identification.tool_specific

Methods in com.compomics.util.parameters.identification.tool_specific with parameters of type DigestionParameters

Modifier and Type	Method	Description
static String	MyriMatchParameters.enzymeMapping(DigestionParameters digestionPreferences)	Tries to map the utilities enzyme in the digestion preferences to the enzymes supported by MyriMatch.